The article is a little sensationalized. Steganography/obfuscation only works when the tool used is kept between both sender and receiver, once the tool is available to all its method and function can be attacked and compromised. Not to mention you as an end user utilizing an ISP are limited in the many ways you can send/receive traffic over certain ports/protocols for various security reasons.

In my opinion a VPN that utilizes a sound encryption implementation would be the best way to go. Keeping in mind of course the USA is not the only country that conducts SIGINT.